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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2022-03-15, 10:26 based on data in: /home/jhetzler/MiSeqOSL/trm/fastqc


        General Statistics

        Showing 400/400 rows and 3/5 columns.
        Sample Name% Dups% GCM Seqs
        A10_R1
        87.9%
        44%
        0.0
        A10_R2
        93.0%
        41%
        0.0
        A11_R1
        87.4%
        47%
        0.0
        A11_R2
        93.4%
        43%
        0.0
        A12_R1
        94.9%
        54%
        0.0
        A12_R2
        97.4%
        49%
        0.0
        A13_R1
        81.3%
        38%
        0.0
        A13_R2
        86.6%
        36%
        0.0
        A14_R1
        83.1%
        39%
        0.0
        A14_R2
        88.2%
        37%
        0.0
        A15_R1
        83.9%
        40%
        0.0
        A15_R2
        90.2%
        37%
        0.0
        A16_R1
        86.6%
        41%
        0.0
        A16_R2
        91.4%
        38%
        0.0
        A17_R1
        84.5%
        40%
        0.0
        A17_R2
        89.5%
        38%
        0.0
        A18_R1
        83.3%
        39%
        0.0
        A18_R2
        89.6%
        37%
        0.0
        A19_R1
        81.1%
        40%
        0.0
        A19_R2
        85.8%
        37%
        0.0
        A1_R1
        89.9%
        47%
        0.0
        A1_R2
        93.9%
        44%
        0.0
        A20_R1
        85.8%
        39%
        0.0
        A20_R2
        91.0%
        37%
        0.0
        A21_R1
        84.3%
        40%
        0.0
        A21_R2
        89.1%
        38%
        0.0
        A22_R1
        85.4%
        40%
        0.0
        A22_R2
        89.7%
        38%
        0.0
        A23_R1
        84.0%
        39%
        0.0
        A23_R2
        90.1%
        37%
        0.0
        A24_R1
        82.1%
        40%
        0.0
        A24_R2
        87.5%
        38%
        0.0
        A25_R1
        85.9%
        39%
        0.0
        A25_R2
        90.7%
        36%
        0.0
        A26_R1
        84.0%
        39%
        0.0
        A26_R2
        89.4%
        37%
        0.0
        A27_R1
        84.1%
        40%
        0.0
        A27_R2
        89.6%
        37%
        0.0
        A28_R1
        90.4%
        52%
        0.0
        A28_R2
        93.6%
        47%
        0.0
        A29_R1
        84.4%
        39%
        0.0
        A29_R2
        90.0%
        37%
        0.0
        A2_R1
        69.5%
        30%
        0.0
        A2_R2
        82.9%
        30%
        0.0
        A30_R1
        83.5%
        41%
        0.0
        A30_R2
        89.8%
        38%
        0.0
        A31_R1
        83.6%
        40%
        0.0
        A31_R2
        89.6%
        38%
        0.0
        A32_R1
        83.9%
        40%
        0.0
        A32_R2
        88.4%
        38%
        0.0
        A33_R1
        79.0%
        41%
        0.0
        A33_R2
        83.1%
        38%
        0.0
        A34_R1
        79.8%
        41%
        0.0
        A34_R2
        83.8%
        38%
        0.0
        A35_R1
        84.4%
        41%
        0.0
        A35_R2
        89.6%
        38%
        0.0
        A36_R1
        78.4%
        40%
        0.0
        A36_R2
        86.3%
        37%
        0.0
        A37_R1
        85.8%
        39%
        0.0
        A37_R2
        90.6%
        37%
        0.0
        A38_R1
        85.5%
        40%
        0.0
        A38_R2
        90.1%
        37%
        0.0
        A39_R1
        84.1%
        41%
        0.0
        A39_R2
        85.2%
        38%
        0.0
        A3_R1
        86.8%
        45%
        0.0
        A3_R2
        92.2%
        42%
        0.0
        A40_R1
        80.0%
        40%
        0.0
        A40_R2
        85.6%
        37%
        0.0
        A41_R1
        86.0%
        39%
        0.0
        A41_R2
        89.9%
        37%
        0.0
        A42_R1
        84.7%
        39%
        0.0
        A42_R2
        88.7%
        37%
        0.0
        A43_R1
        81.5%
        40%
        0.0
        A43_R2
        85.4%
        37%
        0.0
        A44_R1
        84.6%
        38%
        0.0
        A44_R2
        89.2%
        36%
        0.0
        A45_R1
        85.7%
        43%
        0.0
        A45_R2
        89.9%
        40%
        0.0
        A46_R1
        85.6%
        39%
        0.0
        A46_R2
        90.7%
        37%
        0.0
        A47_R1
        84.3%
        39%
        0.0
        A47_R2
        89.6%
        37%
        0.0
        A48_R1
        82.8%
        39%
        0.0
        A48_R2
        88.6%
        37%
        0.0
        A49_R1
        79.3%
        39%
        0.0
        A49_R2
        83.7%
        37%
        0.0
        A4_R1
        86.8%
        44%
        0.0
        A4_R2
        92.4%
        40%
        0.0
        A50_R1
        83.3%
        39%
        0.0
        A50_R2
        87.8%
        37%
        0.0
        A5_R1
        88.7%
        46%
        0.0
        A5_R2
        94.1%
        43%
        0.0
        A6_R1
        88.2%
        44%
        0.0
        A6_R2
        93.4%
        41%
        0.0
        A7_R1
        87.3%
        47%
        0.0
        A7_R2
        93.5%
        43%
        0.0
        A8_R1
        76.1%
        50%
        0.0
        A8_R2
        89.3%
        45%
        0.0
        A9_R1
        87.9%
        45%
        0.0
        A9_R2
        93.1%
        42%
        0.0
        B10_R1
        85.6%
        46%
        0.0
        B10_R2
        92.1%
        43%
        0.0
        B11_R1
        85.1%
        44%
        0.0
        B11_R2
        92.1%
        41%
        0.0
        B12_R1
        72.5%
        30%
        0.0
        B12_R2
        84.7%
        30%
        0.0
        B13_R1
        82.1%
        39%
        0.0
        B13_R2
        87.3%
        37%
        0.0
        B14_R1
        81.2%
        38%
        0.0
        B14_R2
        87.2%
        36%
        0.0
        B15_R1
        76.9%
        39%
        0.0
        B15_R2
        83.1%
        36%
        0.0
        B16_R1
        83.6%
        37%
        0.0
        B16_R2
        88.7%
        35%
        0.0
        B17_R1
        83.5%
        37%
        0.0
        B17_R2
        88.5%
        36%
        0.0
        B18_R1
        83.7%
        38%
        0.0
        B18_R2
        88.6%
        36%
        0.0
        B19_R1
        83.7%
        37%
        0.0
        B19_R2
        88.6%
        36%
        0.0
        B1_R1
        86.4%
        42%
        0.0
        B1_R2
        90.9%
        39%
        0.0
        B20_R1
        82.2%
        37%
        0.0
        B20_R2
        87.8%
        35%
        0.0
        B21_R1
        81.4%
        34%
        0.0
        B21_R2
        86.9%
        33%
        0.0
        B22_R1
        81.8%
        34%
        0.0
        B22_R2
        87.7%
        33%
        0.0
        B23_R1
        84.5%
        37%
        0.0
        B23_R2
        89.0%
        35%
        0.0
        B24_R1
        85.3%
        37%
        0.0
        B24_R2
        90.6%
        35%
        0.0
        B25_R1
        83.1%
        37%
        0.0
        B25_R2
        88.6%
        36%
        0.0
        B26_R1
        84.3%
        38%
        0.0
        B26_R2
        89.6%
        36%
        0.0
        B27_R1
        84.4%
        37%
        0.0
        B27_R2
        89.2%
        36%
        0.0
        B28_R1
        84.6%
        36%
        0.0
        B28_R2
        90.0%
        35%
        0.0
        B29_R1
        70.8%
        37%
        0.1
        B29_R2
        79.1%
        34%
        0.1
        B2_R1
        85.1%
        42%
        0.0
        B2_R2
        91.0%
        39%
        0.0
        B30_R1
        82.6%
        36%
        0.0
        B30_R2
        89.2%
        35%
        0.0
        B31_R1
        84.6%
        37%
        0.0
        B31_R2
        89.3%
        36%
        0.0
        B32_R1
        84.2%
        39%
        0.0
        B32_R2
        88.7%
        37%
        0.0
        B33_R1
        84.3%
        39%
        0.0
        B33_R2
        88.9%
        37%
        0.0
        B34_R1
        78.9%
        40%
        0.0
        B34_R2
        85.8%
        37%
        0.0
        B35_R1
        84.7%
        37%
        0.0
        B35_R2
        89.9%
        36%
        0.0
        B36_R1
        81.9%
        38%
        0.0
        B36_R2
        87.9%
        36%
        0.0
        B37_R1
        80.1%
        39%
        0.0
        B37_R2
        87.0%
        36%
        0.0
        B38_R1
        82.5%
        40%
        0.0
        B38_R2
        88.7%
        38%
        0.0
        B39_R1
        82.6%
        40%
        0.0
        B39_R2
        87.2%
        38%
        0.0
        B3_R1
        83.7%
        49%
        0.0
        B3_R2
        91.4%
        45%
        0.0
        B40_R1
        86.4%
        41%
        0.0
        B40_R2
        90.8%
        39%
        0.0
        B41_R1
        78.2%
        44%
        0.0
        B41_R2
        83.8%
        41%
        0.0
        B42_R1
        81.7%
        40%
        0.0
        B42_R2
        87.0%
        38%
        0.0
        B43_R1
        80.3%
        39%
        0.0
        B43_R2
        88.4%
        37%
        0.0
        B44_R1
        82.7%
        40%
        0.0
        B44_R2
        88.5%
        37%
        0.0
        B45_R1
        82.3%
        39%
        0.0
        B45_R2
        87.6%
        36%
        0.0
        B46_R1
        80.2%
        39%
        0.0
        B46_R2
        85.7%
        36%
        0.0
        B47_R1
        80.5%
        40%
        0.0
        B47_R2
        86.4%
        37%
        0.0
        B48_R1
        79.9%
        40%
        0.0
        B48_R2
        87.3%
        38%
        0.0
        B49_R1
        81.6%
        40%
        0.0
        B49_R2
        89.0%
        38%
        0.0
        B4_R1
        86.5%
        42%
        0.0
        B4_R2
        91.8%
        40%
        0.0
        B50_R1
        78.3%
        37%
        0.0
        B50_R2
        86.2%
        36%
        0.0
        B5_R1
        84.0%
        45%
        0.0
        B5_R2
        90.7%
        42%
        0.0
        B6_R1
        86.3%
        45%
        0.0
        B6_R2
        92.3%
        41%
        0.0
        B7_R1
        88.2%
        52%
        0.0
        B7_R2
        93.2%
        47%
        0.0
        B8_R1
        83.4%
        44%
        0.0
        B8_R2
        90.5%
        41%
        0.0
        B9_R1
        85.1%
        42%
        0.0
        B9_R2
        91.3%
        39%
        0.0
        C10_R1
        87.0%
        39%
        0.0
        C10_R2
        91.8%
        37%
        0.0
        C11_R1
        86.6%
        40%
        0.0
        C11_R2
        91.6%
        37%
        0.0
        C12_R1
        86.7%
        38%
        0.0
        C12_R2
        91.3%
        36%
        0.0
        C13_R1
        86.9%
        39%
        0.0
        C13_R2
        91.4%
        37%
        0.0
        C14_R1
        85.8%
        39%
        0.0
        C14_R2
        91.0%
        37%
        0.0
        C15_R1
        87.3%
        39%
        0.0
        C15_R2
        91.9%
        37%
        0.0
        C16_R1
        86.3%
        37%
        0.0
        C16_R2
        91.1%
        36%
        0.0
        C17_R1
        83.3%
        37%
        0.0
        C17_R2
        88.9%
        35%
        0.0
        C18_R1
        77.3%
        41%
        0.0
        C18_R2
        84.5%
        38%
        0.0
        C19_R1
        84.9%
        39%
        0.0
        C19_R2
        90.5%
        37%
        0.0
        C1_R1
        83.7%
        41%
        0.0
        C1_R2
        89.8%
        38%
        0.0
        C20_R1
        84.8%
        39%
        0.0
        C20_R2
        90.5%
        36%
        0.0
        C21_R1
        81.5%
        41%
        0.0
        C21_R2
        88.4%
        38%
        0.0
        C22_R1
        83.5%
        40%
        0.0
        C22_R2
        89.3%
        37%
        0.0
        C23_R1
        86.8%
        40%
        0.0
        C23_R2
        91.9%
        38%
        0.0
        C24_R1
        85.9%
        40%
        0.0
        C24_R2
        91.3%
        37%
        0.0
        C25_R1
        79.1%
        42%
        0.0
        C25_R2
        83.4%
        39%
        0.0
        C26_R1
        83.8%
        40%
        0.0
        C26_R2
        89.8%
        37%
        0.0
        C27_R1
        81.8%
        40%
        0.0
        C27_R2
        88.6%
        37%
        0.0
        C28_R1
        85.4%
        40%
        0.0
        C28_R2
        90.6%
        38%
        0.0
        C29_R1
        83.7%
        40%
        0.0
        C29_R2
        88.3%
        38%
        0.0
        C2_R1
        83.5%
        42%
        0.0
        C2_R2
        89.6%
        40%
        0.0
        C30_R1
        83.4%
        40%
        0.0
        C30_R2
        87.5%
        38%
        0.0
        C31_R1
        89.5%
        46%
        0.0
        C31_R2
        92.9%
        44%
        0.0
        C32_R1
        84.5%
        41%
        0.0
        C32_R2
        90.5%
        39%
        0.0
        C33_R1
        84.6%
        41%
        0.0
        C33_R2
        90.2%
        39%
        0.0
        C34_R1
        80.0%
        43%
        0.0
        C34_R2
        85.7%
        40%
        0.0
        C35_R1
        83.0%
        44%
        0.0
        C35_R2
        89.7%
        41%
        0.0
        C36_R1
        84.5%
        40%
        0.0
        C36_R2
        89.4%
        37%
        0.0
        C37_R1
        85.1%
        40%
        0.0
        C37_R2
        90.0%
        38%
        0.0
        C38_R1
        83.9%
        40%
        0.0
        C38_R2
        88.9%
        38%
        0.0
        C39_R1
        85.1%
        41%
        0.0
        C39_R2
        89.7%
        38%
        0.0
        C3_R1
        81.6%
        43%
        0.0
        C3_R2
        89.0%
        40%
        0.0
        C40_R1
        84.3%
        44%
        0.0
        C40_R2
        90.0%
        40%
        0.0
        C41_R1
        80.2%
        30%
        0.0
        C41_R2
        86.5%
        30%
        0.0
        C42_R1
        76.9%
        31%
        0.0
        C42_R2
        85.4%
        31%
        0.0
        C43_R1
        77.2%
        32%
        0.0
        C43_R2
        84.4%
        31%
        0.0
        C44_R1
        76.4%
        31%
        0.0
        C44_R2
        83.7%
        31%
        0.0
        C45_R1
        73.6%
        32%
        0.0
        C45_R2
        80.1%
        31%
        0.0
        C46_R1
        76.5%
        31%
        0.0
        C46_R2
        83.3%
        31%
        0.0
        C47_R1
        80.3%
        31%
        0.0
        C47_R2
        87.5%
        30%
        0.0
        C48_R1
        77.7%
        31%
        0.0
        C48_R2
        83.7%
        30%
        0.0
        C49_R1
        83.8%
        40%
        0.0
        C49_R2
        89.4%
        38%
        0.0
        C4_R1
        84.2%
        38%
        0.0
        C4_R2
        89.1%
        36%
        0.0
        C50_R1
        82.6%
        40%
        0.0
        C50_R2
        88.0%
        38%
        0.0
        C5_R1
        84.4%
        38%
        0.0
        C5_R2
        90.2%
        36%
        0.0
        C6_R1
        83.0%
        39%
        0.0
        C6_R2
        88.3%
        37%
        0.0
        C7_R1
        85.1%
        39%
        0.0
        C7_R2
        90.5%
        37%
        0.0
        C8_R1
        86.7%
        39%
        0.0
        C8_R2
        91.6%
        37%
        0.0
        C9_R1
        87.1%
        38%
        0.0
        C9_R2
        91.7%
        36%
        0.0
        D10_R1
        84.4%
        38%
        0.0
        D10_R2
        89.8%
        36%
        0.0
        D11_R1
        83.2%
        38%
        0.0
        D11_R2
        88.3%
        36%
        0.0
        D12_R1
        82.9%
        39%
        0.0
        D12_R2
        87.3%
        36%
        0.0
        D13_R1
        84.6%
        38%
        0.0
        D13_R2
        89.8%
        37%
        0.0
        D14_R1
        82.3%
        39%
        0.0
        D14_R2
        88.5%
        37%
        0.0
        D15_R1
        77.9%
        40%
        0.0
        D15_R2
        84.5%
        37%
        0.0
        D16_R1
        85.7%
        38%
        0.0
        D16_R2
        91.6%
        36%
        0.0
        D17_R1
        82.5%
        40%
        0.0
        D17_R2
        88.6%
        37%
        0.0
        D18_R1
        84.1%
        39%
        0.0
        D18_R2
        89.8%
        37%
        0.0
        D19_R1
        71.9%
        40%
        0.0
        D19_R2
        76.2%
        37%
        0.0
        D1_R1
        86.9%
        41%
        0.0
        D1_R2
        90.9%
        39%
        0.0
        D20_R1
        84.9%
        38%
        0.0
        D20_R2
        89.9%
        37%
        0.0
        D21_R1
        81.2%
        40%
        0.0
        D21_R2
        85.6%
        37%
        0.0
        D22_R1
        76.6%
        41%
        0.0
        D22_R2
        81.1%
        38%
        0.0
        D23_R1
        85.4%
        38%
        0.0
        D23_R2
        90.3%
        36%
        0.0
        D24_R1
        79.6%
        43%
        0.0
        D24_R2
        78.7%
        39%
        0.0
        D25_R1
        83.1%
        36%
        0.0
        D25_R2
        86.1%
        34%
        0.0
        D26_R1
        83.0%
        37%
        0.0
        D26_R2
        88.8%
        35%
        0.0
        D27_R1
        80.7%
        38%
        0.0
        D27_R2
        86.0%
        36%
        0.0
        D28_R1
        81.6%
        38%
        0.0
        D28_R2
        86.3%
        36%
        0.0
        D29_R1
        74.3%
        44%
        0.0
        D29_R2
        73.5%
        40%
        0.0
        D2_R1
        80.1%
        40%
        0.0
        D2_R2
        84.5%
        37%
        0.0
        D30_R1
        83.2%
        38%
        0.0
        D30_R2
        89.1%
        36%
        0.0
        D31_R1
        83.0%
        39%
        0.0
        D31_R2
        88.0%
        37%
        0.0
        D32_R1
        79.7%
        39%
        0.0
        D32_R2
        84.0%
        37%
        0.0
        D33_R1
        79.5%
        38%
        0.0
        D33_R2
        84.4%
        36%
        0.0
        D34_R1
        82.4%
        39%
        0.0
        D34_R2
        87.8%
        36%
        0.0
        D35_R1
        82.6%
        38%
        0.0
        D35_R2
        87.6%
        36%
        0.0
        D36_R1
        81.6%
        38%
        0.0
        D36_R2
        88.4%
        36%
        0.0
        D37_R1
        81.3%
        39%
        0.0
        D37_R2
        87.0%
        36%
        0.0
        D38_R1
        72.9%
        40%
        0.0
        D38_R2
        78.9%
        37%
        0.0
        D39_R1
        85.5%
        39%
        0.0
        D39_R2
        89.0%
        37%
        0.0
        D3_R1
        80.8%
        41%
        0.0
        D3_R2
        83.0%
        38%
        0.0
        D40_R1
        83.0%
        40%
        0.0
        D40_R2
        89.1%
        37%
        0.0
        D41_R1
        83.5%
        40%
        0.0
        D41_R2
        87.8%
        38%
        0.0
        D42_R1
        70.8%
        40%
        0.0
        D42_R2
        75.3%
        37%
        0.0
        D43_R1
        84.9%
        40%
        0.0
        D43_R2
        88.5%
        37%
        0.0
        D44_R1
        63.0%
        43%
        0.0
        D44_R2
        79.9%
        39%
        0.0
        D45_R1
        73.4%
        40%
        0.0
        D45_R2
        79.2%
        38%
        0.0
        D46_R1
        79.8%
        40%
        0.0
        D46_R2
        79.7%
        37%
        0.0
        D47_R1
        79.5%
        38%
        0.0
        D47_R2
        84.7%
        36%
        0.0
        D48_R1
        82.9%
        38%
        0.0
        D48_R2
        90.3%
        36%
        0.0
        D49_R1
        81.5%
        40%
        0.0
        D49_R2
        87.9%
        38%
        0.0
        D4_R1
        84.7%
        38%
        0.0
        D4_R2
        90.0%
        36%
        0.0
        D50_R1
        80.9%
        39%
        0.0
        D50_R2
        87.1%
        37%
        0.0
        D5_R1
        84.7%
        38%
        0.0
        D5_R2
        90.2%
        36%
        0.0
        D6_R1
        84.4%
        38%
        0.0
        D6_R2
        89.7%
        36%
        0.0
        D7_R1
        84.5%
        38%
        0.0
        D7_R2
        89.6%
        36%
        0.0
        D8_R1
        85.8%
        40%
        0.0
        D8_R2
        91.0%
        38%
        0.0
        D9_R1
        78.3%
        39%
        0.0
        D9_R2
        84.2%
        37%
        0.0

        FastQC

        FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (eg PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Overrepresented sequences

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as over represented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all of the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Flat image plot. Toolbox functions such as highlighting / hiding samples will not work (see the docs).


        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

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